Does the email get sent with the internal link, even when you request the user through the external link?

The way to guarantee the url that is sent (as well as change the email to your liking) is to edit the templates under layouts\FBA\emails and hard code the urls. To ensure that your layout does not get overwritten when you upgrade, make a copy of the template
and point to it in the FBA Site Configuration page.

Glad to hear you found a solution. Regarding you question about different templates for each web application: yes you can! Just create separate template files for each web application, and then point to the appropriate file from the fba site configuration
page for each web application.